Long-read sequencing and optical genome mapping technologies have the ability to detect large and complex structural variants. This has led to the discovery of novel pathogenic variants in neurodegenerative movement disorders. Thus, we aimed to systematically compare the SV detection capabilities of OGM and ONT in Parkinson's disease. Ultra-high molecular weight DNA was derived from blood and fibroblast cultures of 19 patients with mostly early-onset Parkinson's disease, and used for Nanopore sequencing and optical genome mapping. The size distributions of deletions and insertions were compared, and variants were filtered for rare or potentially pathogenic variants in 134 known movement disorder genes. Both methods identified SVs > 50 kb; however, optical mapping identified fewer structural variants (49,677) compared to Nanopore sequencing (94,400), but detected six times more in the range 50-80 kb. In general, it detected significantly larger deletions and insertions (p < 2.2 × 10-16). Both methods detected a benign intergenic deletion (195 kb) near ITPR1, and optical mapping validated a previously published 7-Mb PRKN inversion. Small heterozygous deletions in ATXN2, SUCLA2, and PNKD detected by optical mapping were identified to be intronic by Nanopore sequencing. No causal variants were identified in movement disorder genes. Optical mapping can be a powerful first-line method for detecting large structural variants, but it requires a high-resolution method to refine breakpoint positions. Despite certain limitations, Nanopore sequencing was highly capable of detecting large variants independently and allows for a highly complementary assessment and validation of structural variation in combination with optical mapping.

Acute myeloid leukaemia (AML) risk stratification relies on cytogenetic and molecular abnormalities defined by European LeukemiaNet (ELN) 2022. Conventional cytogenetic techniques, including chromosomal banding analysis (CBA) and fluorescence insitu hybridization, have limited resolution and may miss cryptic events. Optical genome mapping (OGM) is a genome-wide approach capable of detecting balanced and unbalanced structural variants with high resolution, potentially revealing cryptic abnormalities of diagnostic and prognostic relevance. We retrospectively studied 100 adults with newly diagnosed AML, each showing one to two cytogenetic abnormalities and lacking the World Health Organization 2022-defining rearrangements or baseline ELN adverse karyotypes. OGM was performed to evaluate additional cytogenetic abnormalities and impact on ELN 2022 risk classification. Clinical outcomes were explored descriptively. OGM detected 91.4% of abnormalities identified by CBA and provided additional information in 37% (95% confidence interval: 28%-47%) of patients. Fourteen per cent was reclassified to an unfavourable cytogenetic group, and 7.7% was reclassified to ELN 2022 adverse risk. Cryptic KMT2A and NUP98 lesions were found in 10% of cases, highlighting potential therapeutic targets. Survival analyses suggested a trend towards poorer outcomes in patients reclassified as adverse, though the small sample limits definitive conclusions. In low-complexity AML, OGM provides substantial incremental diagnostic value, detecting cryptic high-risk and targetable abnormalities, supporting its use as a complementary tool.

Selectivity Filter Mutation in NaV1.5 Promotes Ventricular Tachycardia.

Combined genomic profiling by exome sequencing analysis and optical genome mapping reveals bi-allelic somatic inactivation of SMAD4 in pediatric colon adenocarcinoma.

Copy-Neutral Loss of Heterzygosity in Myelofibrosis: Parallel Evaluation with Optical Genome Mapping and Single-Nucleotide Polymorphism Arrays.

Optical Mapping of Atrial Electrophysiological and Calcium Handling Abnormalities in a Rat Model of Sterile Pericarditis

Optical manometry provides noncontact pressure sensing but remains vulnerable to temperature-induced drift, where thermal expansion and nonradiative relaxation distort luminescence spectra and kinetics. We develop a spectro-temporal ratiometric approach that combines spectral and time-gated luminescence channels to decouple pressure and temperature responses and realize thermally invariant optical manometry. Using Y3In2Ga3O12:Cr3+ as a rigid-lattice host (Dq/B ≈ 2.2), lattice stiffness minimizes thermal sensitivity SR,T, while ratiometric detection stabilizes pressure sensitivity SR,p. The resulting thermal-invariance manometric factor (TIMF) = SR,p/SR,T reaches ≈7700K·GPa-1 in the spectral domain and ≈2500 K·GPa-1 in the time-gated domain, with SR,p up to 51%·GPa-1. These values exceed ruby benchmarks by two orders of magnitude and surpass conventional lifetime analysis by ∼40 times, enabling accurate, self-referenced optical pressure mapping under extreme thermo-mechanical conditions. This work provides luminescent manometry from empirical calibration to a quantitative framework for thermally reliable sensing in coupled fields.

This study aimed to evaluate the clinical value of integrating optical genome mapping (OGM) with conventional genetic methods in the diagnosis of families with spontaneous abortion or offspring abnormalities. Herein, 24 families were included. Genetic testing was first applied in fetuses and children according to indications if samples were available. A parental study was then conducted using OGM with or without conventional methods. In total, 76 samples (28 samples of fetuses and children from 20 families and 48 samples of all 24 parents) were investigated. Clinically reported variants were identified in 21 (21/28, 75.0%) fetuses and children from 17 (17/20, 85.0%) families. OGM with or without conventional methods detected 16 (16/24, 66.7%) clinically reported variants in either parent, including five submicroscopic balanced translocations, two microscopic balanced translocations, four complex chromosomal rearrangements, two D4Z4 repeat contraction disorders, and three variants of uncertain significance (VOUS). Additionally, variations detected in fetuses and children from three (3/24, 12.5%) families were determined to be de novo by OGM. OGM identified structural variations (SVs) out of the detection range of conventional methods and provided structure and breakpoint information to improve clinical interpretation. This study illustrates that integrating OGM with conventional methods is a feasible and powerful strategy in families with spontaneous abortion or offspring abnormalities.

Background: Heart rhythm disturbances remain a serious problem in modern cardiology. Traditional pacemakers have certain limitations including invasiveness, risk of infection, mechanical complications, and a limited service life. Advances in bioengineering and optogenetics technologies offers new prospects for the production of minimally invasive, biocompatible, and controllable cardiac pacing systems. The combination of cell therapy and optogenetics enables to create a photo-controlled biological pacemaker, free from the key drawbacks of traditional devices. Objective: The aim of this study was to produce photosensitive cellular patches and to further investigate their functionality as an optogenetic tissue-engineered pacemaker in an ex vivo rat heart model. Methods: We engineered a cell-based construct using either human cardiomyocytes derived from induced pluripotent stem cells or neonatal rat cardiomyocytes expressing channelrhodopsin-2. These cells were seeded onto fibrous scaffolds made of poly-L-lactic acid and collagen, coated with fibronectin. The testing model was an isolated, temporarily maintained ex vivo rat heart. Optical mapping of calcium activity was used to record cardiac electrophysiology. Results: Functional coupling between the implanted patch and the host myocardium was observed 35 minutes after implantation. Photostimulation reliably increased the heart rate, which was confirmed by stochastic dominance analysis. The experiments in vitro on cell cultures demonstrated the operational capacity of channelrhodopsin-2 upon illumination with 470 nm light. Conclusion: This study successfully demonstrates a complete technology cycle, from the genetic modification of cells to the control of contractions in a whole organ. It represents a significant step towards developing targeted and safe methods for future temporary cardiac pacing. Our results confirm the fundamental feasibility of a hybrid optogenetic approach and lay the groundwork for further research into creating safe, controllable, and biocompatible next-generation pacemaker systems.

BackgroundOptical genome mapping (OGM) is an emerging cytogenetic method for concurrently detecting structural variants (SVs) and copy number variants (CNVs). However, its clinical application in prenatal diagnosis remains underexplored.MethodsThis study retrospectively evaluated the clinical validity of OGM in prenatal diagnosis by comparing with two routine genetic testing methods: karyotyping and chromosomal microarray analysis (CMA). Both positive and negative cases detected by routine genetic methods were enrolled to evaluate the technical concordance of OGM and its capability to improve diagnostic rate in negative cases. The exclusion criteria were balanced centromeric translocations, mosaic cases with cellular fractions < 20%, and loss of heterozygosity (LOH) < 25 Mb. All samples subjected to OGM testing were anonymized and analyzed blindly. The results from OGM were compared with those from routine genetic testing, and statistical analyses were performed to assess technical concordance and diagnostic rate.ResultsOf 217 samples (166 positive samples and 51 negative samples for routine genetic testing), all were successfully tested with OGM, including 2 umbilical cord blood samples, 4 chorionic villi samples, and 211 cultured amniotic fluid samples. Of the 207 reportable chromosomal aberrations from 166 positive samples, the blinded concordance between OGM and CMA, karyotyping, and combination of karyotyping plus CMA was 97.81%, 96.36%, and 97.10%, respectively. OGM missed six aberrations initially, including one LOH, two marker chromosomes, and three microdeletions. However, after reanalysis, its concordance improved to 100% with CMA and 99.03% with karyotyping plus CMA. OGM also diagnosed one additional case of a 3-kb deletion in 51 negative samples, improving the diagnostic rate by 1.96%. Moreover, OGM reclassified the pathogenicity of two microdeletions from pathogenic to uncertain significance in 2 positive cases. Furthermore, OGM clarified the diagnosis suspected by routine genetic testing and improved diagnostic accuracy in some cases.ConclusionAs far as we know, this is the largest retrospective study on OGM in prenatal diagnosis, and it includes a broad range of sample types. The results showed that OGM exhibits high concordance among the tested methods and increases the diagnostic rate. Thus, OGM has the potential to become a first-line technique for prenatal diagnosis in the future.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12967-025-06901-9.

Background: Optical genome mapping (OGM) detects genome-wide structural variants (SVs), including balanced rearrangements and complex copy-number alterations beyond standard-of-care cytogenomic assays. In chronic lymphocytic leukemia (CLL), cytogenetic and genomic risk stratification is traditionally based on fluorescence in situ hybridization (FISH), karyotyping, targeted next-generation sequencing (NGS), and immunogenetic assessment of immunoglobulin heavy chain variable region (IGHV) somatic hypermutation status, each of which interrogates only a limited aspect of disease biology. Methods: We retrospectively evaluated fifty patients with CLL using OGM and integrated these findings with cytogenomics, targeted NGS, IGHV mutational status, and clinical time-to-first-treatment (TTFT) data. Structural variants were detected using OGM and pathogenic NGS variants were derived from a clinical heme malignancy panel. Clinical outcomes were extracted from the electronic medical record. Results: OGM identified reportable structural variants in 82% (41/50) of cases. The most frequent abnormality was del(13q), observed in 29/50 (58%) and comprising 73% (29/40) of all OGM-detected deletions with pathologic significance. Among these, 12/29 (42%) represented large RB1-spanning deletions, while 17/29 (58%) were focal deletions restricted to the miR15a/miR16-1 minimal region, mapping to the non-coding host gene DLEU2. Co-occurrence of adverse lesions, including deletion 11q/ATM, BIRC3 loss, trisomy 12, and deletion 17p/TP53, were recurrent and strongly associated with shorter TTFT. OGM also uncovered multiple cryptic rearrangements involving chromosomal loci that are not represented in the canonical CLL FISH probe panel, including IGL::CCND1, IGH::BCL2, IGH::BCL11A, IGH::BCL3, and multi-chromosomal copy-number complexity. IGHV data were available in 37/50 (74%) of patients; IGHV-unmutated status frequently co-segregated with OGM-defined high-risk profiles (del(11q), del(17p), trisomy 12 with secondary hits, and complex genomes whereas mutated IGHV predominated in OGM-negative or structurally simple del(13q) cases and aligned with indolent TTFT. Integration of OGM with NGS further improved genomic risk classification, particularly in cases with discordant or inconclusive routine testing. Conclusions: OGM provides a comprehensive, genome-wide view of structural variation in CLL, resolving deletion architecture, identifying cryptic translocations, and defining complex multi-hit genomic profiles that tracked closely with clinical behavior. Combining OGM and NGS analysis refined risk stratification beyond standard FISH panels and supports more precise, individualized management strategies in CLL. Prospective studies are warranted to evaluate the clinical utility of OGM-guided genomic profiling in contemporary treatment paradigms.

Optical genome mapping (OGM) has demonstrated significant potential in detecting structural variations (SVs) and has been comprehensively evaluated both retrospectively and prospectively in prenatal diagnosis. However, obtaining an adequate volume of amniotic fluid (AF) samples for OGM remains challenging due to the diverse detection techniques currently employed in prenatal diagnosis, which can limit the applicability of OGM in this setting. This study seeks to explore enhancements in cell culture techniques and quality control processes for prenatal samples when utilizing OGM in prenatal diagnosis. OGM successfully analyzed 188 AF samples with a minimum input of 0.225million cells for ultra-high-molecular-weight DNA extraction. The study provides a comprehensive overview of the mass of chorionic villus samples, the volume of AF used for cell culture, the duration of culture, and the cell yields obtained for OGM. It was demonstrated that reducing the number of cells used for DNA isolation may not significantly decrease DNA quality for OGM with optimal cell viability and may even yield better results than those achieved with recommended cell amounts. This suggests that the current QC standards may be overly stringent, and that variant analysis remains feasible for some samples that do not meet these criteria. Based on the variant data analysis of these samples, standards appropriate for prenatal samples were summarized. The findings of this study indicate that a reduced volume of AF sample or a shortened cell culture duration can be achieved in prenatal OGM, thereby enhancing the feasibility of employing OGM in prenatal diagnosis and potentially benefiting patients. Furthermore, data QC metrics suitable for prenatal samples may be more tolerant than previously recommended, necessitating further investigation with larger cohorts to establish specific QC standards for prenatal samples.

KMT2A partial tandem duplication (PTD) occurs in approximately 5-10% of acute myeloid leukemia (AML) cases and is associated with poor prognosis. While its cytogenetic and molecular features are well described, the immunophenotypic characteristics of AML with KMT2A-PTD remain incompletely defined. We identified 47 cases of AML with KMT2A-PTD by optical genome mapping. All cases underwent flow cytometric immunophenotypic analysis and next-generation sequencing using an 81-gene panel. The cohort included 32 men and 15 women with a median age of 67 years (range, 19-87). Thirty-eight cases were de novo AML, and nine were secondary to myelodysplastic syndrome and/or myeloproliferative neoplasm. Most cases (93%) demonstrated a normal or non-complex karyotype. The most frequent mutations involved FLT3-ITD (47%), DNMT3A (43%), and RUNX1 (23%). Thirty-one cases (66%) were granulocytic, while 16 (34%) showed granulocytic and/or monocytic differentiation. Blasts uniformly expressed HLA-DR and frequently expressed CD117 (91%) and CD34 (79%). Increased expression of CD123 (74%) and CD117 (43%) and decreased expression of HLA-DR (74%) and CD38 (69%) were common. Aberrant CD25 expression was observed in 51% of cases. Increased CD123 and aberrant CD25 expression were significantly associated with FLT3-ITD mutations (both p < 0.0001) but not with other recurrent mutations. There was no correlation between FLT3-ITD mutation and expression levels of CD117, CD38 or HLA-DR (all p > 0.05). AML with KMT2A-PTD shows distinctive immunophenotypic features with increased CD123 and aberrant CD25 expression, both associated with FLT3-ITD. These markers may have diagnostic and therapeutic relevance in this AML subtype.

Three painted valuable wood sculptures from conventual collections in Apulia (Southern Italy), made between the beginning of the 17th century and the first half of the 18th century, were studied to shed light on the pictorial materials and techniques of the Neapolitan Baroque sculpture in Southern Italy. A multi-analytical approach was implemented using integrated micro-invasive techniques, including polarized light microscopy (PLM) in ultraviolet (UV) and visible (VIS) light, scanning electron microscopy coupled with energy dispersive spectroscopy (SEM-EDS), Fourier-Transform Infrared (FTIR) spectroscopy, and pyrolysis–gas chromatography/high-resolution mass spectrometry (Py-GC/HRMS). The stratigraphic sequences were microscopically identified, and the pictorial layers were discriminated on the basis of optical features, elemental compositions, and mapping. Organic components were detected by FTIR as lipids and proteinaceous compounds for binders, while terpenic resins were detected as varnishes. Accordingly, PY-GC/HRMS identified siccative oils, animal glue, egg, and colophony. The results allowed the identification of the painting techniques used for the pictorial films and the ground preparation layers and supported the distinction between original and repainting layers. The results of this multi-analytical approach provide insights into Baroque wooden sculpture in Southern Italy and offers information to support restorers in conservation works.

Cryptic balanced translocations are a challenging diagnostic dilemma in conventional cytogenetics. This study aimed to evaluate the utility of optical genome mapping (OGM), an emerging technology for detecting structural variations, in resolving such cases among couples with adverse pregnancy outcomes. We performed a retrospective analysis using OGM on three unsolved cases following karyotyping and trio-whole exome sequencing (trio-WES). The cohort included two couples with adverse pregnancy outcomes and a 46,XX SRY+ male. In all three cases where a translocation was clinically suspected but cytogenetically elusive, OGM successfully identified precise cryptic balanced translocations. Crucially, it defined the genomic breakpoints at high resolution. In the case of the 46,XX SRY+ male, OGM identified a cryptic translocation of Yp11.2 into Xp22.3 and the paracentric inversion inv(Y)(p11.2p11.2), explaining the sex reversal phenotype. This study shows that OGM is a valuable adjunctive diagnostic method for detecting cryptic translocations. By providing a molecular diagnosis, it enables definitive reproductive risk assessment and personalized genetic counseling for carrier couples.

In recent years, the quality of genome assemblies has notably improved, primarily due to advances in third-generation sequencing technologies and bioinformatics tools. In the present study, we obtained genome assemblies for two flax (Linum usitatissimum L.) varieties, K-3018 and Svyatogor, using Oxford Nanopore Technologies (ONT) simplex R10.4.1 data and the Hifiasm algorithm optimized for ONT reads. The K-3018 genome assembly was 491.1 Mb and consisted of thirteen full-length chromosomes and two one-gap chromosomes. The Svyatogor genome assembly was 497.8 Mb and consisted of twelve full-length chromosomes and three one-gap chromosomes. All chromosomes had telomeric repeats at their ends for both varieties. Hi-C contact maps and Illumina genomic data supported the accuracy of the obtained assemblies. The K-3018 and Svyatogor genome assemblies surpassed the quality of the best currently available flax genome assembly of variety T397, which serves as a reference for L. usitatissimum in the NCBI Genome database. Comparative analysis revealed that the flax genomes are generally quite similar at the chromosome level, with only a few large-scale differences. Thus, two near-T2T (telomere-to-telomere) flax genomes were assembled from the ONT simplex R10.4.1 reads using Hifiasm ONT without involving Pacific Biosciences (PacBio) HiFi or ultra-long ONT reads as well as optical maps. High-quality flax genomes are essential for improving the efficiency of genetic research, evaluating genetic diversity at the whole-genome level, and developing breeding and genome editing approaches of this valuable multipurpose crop.

Acute myocardial ischemia triggers electrophysiological changes, including altered cardiac action potential and conduction slowing. Optical mapping is widely used to study these changes, but most experiments use excitation-contraction uncouplers to suppress contractile motion and motion artifacts. We hypothesized that contraction suppression with these uncouplers masks ischemic effects, leading to misleading results. We compared Langendorff-perfused, noncontracting hearts treated with blebbistatin to contracting hearts under acute ischemic conditions. Optical mapping with emission ratiometry and motion-tracking postprocessing minimized motion artifacts, whereas ischemia was induced by ligating the obtuse marginal branch of the left circumflex coronary artery. Contracting hearts exhibited faster and more pronounced reductions in action potential duration (APD) and action potential triangulation (2 min vs. 14 min), along with an increased incidence of spatially discordant alternans (SDA). They also displayed steeper APD restitution slopes, whereas these slopes were flattened in noncontracting hearts. These differences may stem from reduced metabolic demands and the absence of mechanoelectric feedback in noncontracting hearts. In contrast, contracting hearts, with higher metabolic activity and mechanical feedback, experienced more severe ischemic changes. These findings highlight the limitations of using blebbistatin-treated, noncontracting hearts in electrophysiological research, as critical ischemic effects may be underestimated. This study underscores the need to integrate mechanical and electrical dynamics in preclinical models to accurately replicate ischemic conditions, enhancing the translational relevance of experimental cardiac research.NEW & NOTEWORTHY This study highlights key differences in acute ischemic responses between contracting and blebbistatin-treated noncontracting rabbit hearts. Contracting hearts showed faster, more severe action potential duration reductions, increased spatially discordant alternans, and steeper restitution slopes, emphasizing the role of mechanoelectric feedback and higher metabolic demands. These findings challenge reliance on noncontracting models in electrophysiological research, underscoring the need for models integrating mechanical and electrical dynamics to improve the translational relevance of ischemic studies.

Optical Genome Mapping in Pediatric Hematologic Malignancies: High Diagnostic Yield and Unique Insights Across Leukemia Subtypes.

Optical mapping in Black genomes: Distinct LCR22 structures and 22q11.2 deletion syndrome mechanisms.

Mitochondrial NOX4 drives atrial fibrillation via redox-dependent structural remodeling and fibrosis.